Some recommendations:

-servlets/jsp : Marty Hall & Larry Brown 's book on servlets/jsp( very good)
-general intro to java : Just Java by VanderLinden( I think)
-for EJB I did not study a book but I had some training material.

Definately use Eclipse as IDE>
Tomcat for servlets/jsp
I used BEA Weblogic for EJB

Vlad